singularity.config

params {
/*
    User setting options (mandatory)
     */
// input file and genome reference()

    fastq_ext = '*_{1,2}.fq.gz'
    fasta_ref = '/data/database/hg38/genome.fa'
    design = 'design.file' // or null
    hisat2_index = '/data/database/hg38/hisatIndex/grch38_snp_tran/genome_snp_tran'
    //human gtf only
    gencode_annotation_gtf = "/data/database/hg38/Annotation/gencode.v24.annotation.gtf"
    lncipedia_gtf = "/data/database/hg38/Annotation/lncipedia_4_0_hg38.gtf" // set "null" if you are going to perform analysis on other species

/*
    User setting options (optional)
     */
    // tools setting
    hisat_strand = 'RF'
    star_index = ''//set if star used
    bowtie2_index = ''//set if tophat used
    aligner = "hisat" // or "star","tophat"
    sam_processor="sambamba"//or "samtools(deprecated)"
    qctools ="fastp"  // or "afterqc","fastp","fastqc","none" to skip qc step
    detools = "edger"//or "deseq2"
    quant = "kallisto"// or 'htseq'
    //other setting
    singleEnd = false
    unstrand = false
    skip_combine = false
    lncRep_Output = 'reporter.html'
    lncRep_theme = 'npg'
    lncRep_cdf_percent = 10
    lncRep_max_lnc_len = 10000
    lncRep_min_expressed_sample = 50
    mem=60
    cpu=30
 /*
    for non-human setting
 */
    species="human"// mouse , zebrafish, fly
    known_coding_gtf=""
    known_lncRNA_gtf=""


/*
Don't modify
*/
    cpatpath ='/opt/CPAT-1.2.3'


}

/*
Don't modify either
*/
// Docker options

singularity.enabled = true
process.container = './lncPipe.image'
singularity.autoMounts = true
// individual process setting
process.cache = 'deep'

process {
    withLabel: para {
        maxForks = 6
    }

    withLabel: 'qc' {
        maxForks = 6
    }

}

manifest {
    homePage = 'https//github.com/likelet/LncPipe'
    description = 'LncPipe:a Nextflow-based Long non-coding RNA analysis PIPELINE'
    mainScript = 'LncRNAanalysisPipe.nf'
}